Thursday, September 20, 2007

Calling All Adaptationists (Again)

Have I got a treat for you! Before getting to the special excitement, let me congratulate all of you adapationists for your outstanding performance in the last contest [Calling All Adaptationists]. You did a marvelous job of making up stories to explain homosexuality in humans. Rudyard Kipling would have been proud [Just-So Stories].

Your mission for today, should you choose to accept it, is to explain odorous urine (smelly pee).

Here's the data. Some people produce odorous urine when they eat asparagus. They can transform the chemical, asparagusic acid (1,2-dithiolane-4-carboxylic acid), into smelly compounds like methanethiol, dimethyl sulfide, dimethyl disulfide, bis(methylthio)methane, dimethyl sulfoxide, and dimethyl sulfone (Mitchell, 2001). Other people can eat asparagus 'till the cows come home and their urine remains as pleasantly smelling as usual. The allele for producing the smell is an autosomal dominant trait.

There's an additional complication. Some people can't smell the odorous urine. There's no linkage between excretors and perceivers (able to smell the urine). Some can excrete but not smell and some can excrete and smell. All permutations exist in the population.

This ability to excrete smelly compounds and the ability to smell them are both examples of visible phenotypes. They're not just some neutral variation hiding away in junk DNA. Therefore, many (most?) adaptationists will certainly insist that it has to have an adaptive role in human evolution.

This is untilled soil, as far as I can gather. For some reason the experts haven't published the explanation. At least there's nothing I could find after hunting on the internet. You could become famous if your story makes sense. Let's see what you can come up with. I'll get you started ....

Once upon a time there were naked hunter men running on the savannah while their gatherer wives collected asparagus in the deep water by the sea shore ....

What makes it an excellent case? As I keep trying to point out (to deaf ears, evidently), nobody fits Dr. Moran's strawman caricature of an adaptationist. I'll cheerfully grant this example, both the production and the detection, as highly probable non-adaptations. For one thing, only people in the eastern Mediterranean region even had the chance to eat asparagus until quite recently.

However, true pluralists would have to agree that we cannot automatically conclude that the production, the perception, and/or the polymorphisms thereof must therefore be due to drift. Before I committed myself to an ultimate explanation, I would want to know more about the enzyme and its recessive allozyme and how else they are used, and I'd be interested in geographical patterns of allele frequencies. I'd want to know what olfactory receptors are involved and what other kinds of chemicals they can detect.

This is not at all like the case of human hairlessness (I'm not touching the homosexuality issue for which, by the way, I doubt a genetic cause); there is good reason to entertain a hypothesis of adaptation in the hairlessness case for reasons I expressed repeatedly on that thread a while back. Ditto for the ABO blood group polymorphism.

Seriously--responsible hypotheses of adaptation are (or ought to be) backed up with plausibility based on biological knowledge. Nobody is going to suggest an adaptationist explanation for the way some people's pee smells (now wolves and rodents on the other hand...). To suggest otherwise is silly.

So, this trait is absurd enough we can all agree it probably does not confer any logic capable of endowing some with greater fitness than others. Good! Because, the truth be told, adaptationism has such an "easy" understanding,we have now a large anglo school dedicated to churning such speculations for every human behavior that they can... all in the name of biology and evolution

How can this offshoot of adaptationism not have a corrosive effect on the perception of science? Aaaah well. Let's juts discuss the scientific part.

Sven, you still seem to be unable to make the distinction between simple positive slection for a trait,wich increases its frequency, vs the cummulative effect of directional selection in the origi of an adaptation. Only in tthe second case does the selective advatage participate in the origin of the adaptation. In the first case, the seective advatage did not participate in the origin of the adaptation, but rather, it is the consewuence of a single event of mutation.

This distinction I have repeated to you in different forms at least three times yet you still show no sign of understanding.

An still no one rises up to the simple challenge I set of providing a single field example of how directional selection produces the origin of an adaptation.

The truth the adaptationists can't handle: that selection may not be a leader, but a follower of organic change.

Sanders: "providing a single field example of how directional selection produces the origin of an adaptation."

The vertebrate eye.

(If anyone attempts to redefine that as ultra-primitive bilateral light sensitive spots and declare that - sans evidence - to be a single mutation, then they would be the ones moving goalposts.)

And you're the one who is confusing origin with adaptive significance. The most orthodox of neo-Darwinians hold that the origin of VARIATION is not adaptive. Unless one accepts Lamarckism (and I won't even rule it out as impossible - depending on definition).

You ought to make clear what you mean by adaptation, since by some definitions any trait variant that confers a selective benefit is technically an adaptation. You obviously mean complex adaptation. (Yes, I do the same thing, referring to adaptation as a complex trait shaped by selection). Can large effect mutations + epigenetic facilitation produce complex features? (Which are themselves subject to modification.) Sure. So can gradual accumulation of mutations over the course of many steps.

There is room for both mutations of large and small effect (and those in between) for having a role in the origin of complex adaptations.

To insist otherwise is just dogmatism.

I'm more of a hardline selectionist/adaptationist than most, since I accept the importance of multilevel selection; characterize neutralism, drift, and systems processes as facilitators of adaptation; and view selection as having a major role in development.

Your views of evolution and biology are nothing but a great cheeseball, tupaia. You substitute ideology for actual biological and evolutionary knowledge.

You think you are the first person to merely point at the vertebrate eye and assume that proves the power of directional selection? Dude, this is NOT the XIXth century. If you were abit more of a "pro" you would understand that I am demanding a FIELD example, where a selective pressure can be seen in action and measured. Obviously I'm thinking of microevolution and relatively simple adaptations; camouflaging pigments, burrowing claw, length of the metatarsal. And then you come up with the eye, a macroevolutionary change, where no such thing as selection in action can be observed.To think that the eye can be presented just like that as an empirical example of the power of directional selection is so stupid at so many levels specially when I have already discussed the many factors other than selection that make complex adaptataions come about. Tupaia, that was an ideological, amateur response. So, it's adios time for you. Take care now, and byebye then.

Unless we observed it happening in real time during the last century or so, we have no way of determining whether selection played a role in the evolution of a trait? Creationists would love those criteria.

MUCH better, Tupaia.I'll even talk to you again, but now you know, never use the eye again.Are these directional accumulations of several genes with a similar effect? have selective advatages been established?I'll even read the amylase reference if you give it to me

I don't think that any evidence for selection becomes inevitably erased beyond a few hundred years ( "you wish", Tupaia)

I am merely demanding the same standard of evidence that has already been provided for the study of the origin of adaptations: They simply do not fit the idea that directional selection leads organic change. These are documented in as short as microbial time ranges. In plants and animals, comparisons are made between sister "species" (fairly recent splits) where crosses are still possible between the different morphs so the genes responsible for the different adaptive "morphs" (or physiologies, etc ) can be hunted down. Molecular resolution of actual genes is completely possible and thus, desirable.

The result: numerous times adaptive differences are tracked down to single or few mutaions mutations with large effecst. Advantages are the cosequences of these mutations; they are not the cause of their origin (unless you think teleologically, a problem that adaptationists tend to develop)

I'm more interested in the case where directional selection is supposed to accumulate genes with small phenotypic effects, to thus produce an important adaptive difference between sibling species. Is that not an unreasonable request? I don't think so. It's totally doable. But the cases right now favors mutationism score are looking like a landslide victory.

As I understand it, the polymorphism is not for the ability to produce the odoriferous compound. Rather it's for the ability to detect this compound.

From my (quick) reading of the literature, I think both traits are present. Biochemical tests of urine have shown the odorous compounds to be present in some people and not in others. (Most of the collection and testing is done by non-perceivers!)

As an amateur I’ve tried boil this debate down to something I understand: My understanding here is that the question really swings around the sensitivity to survival chances of changes in phenotype: I assume that Larry is raising a question over the sensitivity of urine chemistry to survival chances; namely, does it effect survival chances strongly?

Now it would seem to me (and this may be naive as I’m really on this blog to learn) that if one plots phenotypical parameters against survival chances, (such a graph would probably classify as a Dapper) then it seems unlikely to me that all such graphs peak equally as sharply over a narrow range of parameter value. Hence, my guess is that some traits have ‘low humps’ rather than sharp peaks. For example, I have often wondered about the number of digits: why not six or four per limb? I suspect there is no strong selection for plus or minus a digit (Correct me if I am wrong). Like certain technological advances, the initial ‘chance’ legacy got locked in at an early stage and there was no going back.

Now if evolution was a much more vigorous ‘computational’ process and rung the changes and ‘tested’ designs vastly quicker than it does, then perhaps it could have come up with an the octal or hexadecimal solution to the digit issue (that is eight or sixteen fingers instead of ten). In its wake it would have left many failed technological civilizations behind as they gave way to organisms much better adapted to binary computational hardware because they had eight or sixteen tentacles and so were well adapted to the hexadecimal and octal counting systems! (Note: Please turn on your satire alert system before reading that last paragraph!)

I suppose now Sanders'll whine that "selection only modified the jaws!" I can only say that if you don't believe that the various feeding modes of Malawi cichlids constitute adaptations, there's not much hope for you.

From my (quick) reading of the literature, I think both traits are present. Biochemical tests of urine have shown the odorous compounds to be present in some people and not in others. (Most of the collection and testing is done by non-perceivers!)

Aha! There's the key to the adaptationist just-so story! The difference in perception drives selection for sewer workers -- their ability to be resistant to the worst smells is an opportunity for niche selection, and the rise of urbanization has created greater opportunities for people who can handle the odors.

As for the production of those bad smells...umm, tanning. Yeah, that's the ticket. Those compounds have properties that make them more effecting in processing leather. (I know, I'm inventing a property that might not be there -- but it's a question that opens doors for the adaptationist research program.)

Oh, I totally agree about the possibility of human pheromones, but I do doubt that urine is an important medium for their dissemination (axillary and pubic hair on the other hand...still haven't seen any evidence for pedomorphosis).

Sanders, I give up. Believe it or not, you don't know what you're tallking about. If you can entertain for just a second the notion that there might be people in the world that know more than you do about something, I think you could learn a lot from reading this, or pretty much anything by G.C. Williams.Hey, by the way, since you've identified your holy trinity of evolutionary biology, I wonder if you've ever seen this one by Mayr?

Hey, I'm PROUD to say that about the Moray. And watch your ass: I may prove it.

The cichlid paper is pretty close to what I wanted but yet I'm a bit disappointed; They are not talking about a single "trait" but several traits, some metrical, some "geometric". So when they say "we retrieved 46 QTL" it sounds very impressive but actually these are not genes contributing to a single trait, but they are talking about "the oral jaw apparatus" in genral...not precisely a metric trait, huh.

Plus for each trait, the average of the influence of a single QTL is about 35%. So we can say that in average about 3 genes explain all the morphological variation for each trait. They say the influence goes from about 6% to 56%; if the average is 35%, I am guessing that the tendency is for a single QTL to be responsible for a large chunk of the trait.

This is not an irrelevant observation when you take into account that different traits of the OJA are correlated as a result of qtl's that are clustered together ("pleiotropy") This cannot be attributed to directional selection yet it seems to me crucial of you ara arguing that selection is responsible for an "accumulation" of traits. Clustering is a NON-selective explanation as to why sevral traits of the oral jaw apparatus go together; you can think that the same selective pressure has accumulayted them , but the story gets weird if you reaize there is little channce dfor those traits for NOT going together given their position in the genome.

Sanders: "adaptive differences are tracked down to single or few mutaions mutations with large effecst."

Quantify "large effect."

Are dorso-ventral inversion and variant hemoglobin molecules both the result of mutations of "large effect"? If so, is the term "mutation of large effect" even meaningful?

Will you only accept virtually innumerable mutations of infinitesimal effect acting on a single metric of a trait, driven by steady directional selection with no episodic stasis or reversals, as evidence of neo-Darwinism?

And a "FEW mutations"? That's very different than a single macromutational origin of a complex adaptation.

(Quantify "few.")

Isn't that conceding quite a bit?

In fact, I believe that you have conceded the entire argument with the word "few."

Does "mutationism" merely mean that selective pressures themselves do not call beneficial mutations into existence - an assertion that was never part of neo-Darwinism anyway?

Or is "mutationism" the milder claim that there is not operationally infinite variation at all times for selection to act upon? That claim is so mild that it is trivial - because nobody disagrees with it.

How anyone can argue in favor of "mutationism":

1. Invoke "large effect" for all mutations of significant effect. (We're all hopeful monsters here.)2. Invoke pleiotropy until proven otherwise.3. Not pleiotropy? Invoke linkage until proven otherwise. 4. Not linkage? It's only a "few" loci anyway - so the mutationist, not Darwinian, paradigm still holds.5. They're still not buying it? Deny that the feature in question is really a single trait - even if it clearly constitutes a functional complex.

The other papers are also not eloquent enough...for instance, in the amilase case, we can find people with high number of genes in all populations; it is just the average number of genes that is greater in the starch populations. So yeah, selection can make those dudes more frequent and push up the average number of genes in starch populations, but individuals with a high number of these gens can be found anywhere.

And about the high altitude poeple, we have a lot of physiolgicla traits compared between andean, tibetan and normal populations, with some intriguing differences and similarites; but we have not much idea about their genetic underpinnings.

Tibetans show heritability measurements and thus some potential for selection, but intriguingly the andeans do not. While it can be argued that tibetans are "on their way" whereas andean "already got there", specially taking into account that andeans seem to have some traits that suggest a higher efficiency, th fact is that the tibetans have actually been in the hights 10000 years longer than the andeans. Also, some of the differences observed betwee tibetans and andeans have no ready adaptive aexplanation.

If you ask me, these differences have a LOT to do with the pre-existing gene pool of each population at the moment of colonization.

In any case, this study does not have sufficient genetic data; saying something is inheritable and thus could be selected is pretty preliminary. Plus in this case in aprticular, I'm oretty convinced that environment is crucial; that is, whetther your physiology was raised or not in the hights.

That was the nice thing of the cichlid paper: they hunted down the actual genes.

tupaia, by few I mena it is usually a matter of 1-3 genes expaingi the entire variation of the trait. This is usually the case, specially just 1 mutation.plus, this fucntioal complex thing is indeed not put together by selection if different traits of the complex are correlated because of their genomic position. But I guess you just don't understand that point.

let me reverse that answer on you Tupai. Is two rather tha 1 mutations enough to say that selection directed organic change?The truth is, the larger the amount of genes, and the smaller their effects, the happier should the adaptationist be.

Think of the distribution of deleterious, neutral, near-neutral, and beneficial mutations.

Now consider the probability that beneficial alleles of a two loci trait are co-occurring in the absence of selection. In every case. That's a very small number, with factors that include the probability of beneficial mutation and the total number of two loci traits in the entire history of the biota. Are you willing to assert drift or nonadaptive genetic linkage for every case?

Admittedly, in decades past orthodox neo-Darwinism was overly dismissive of (true) mutations of large effect. Selectionism-adaptationism is a big tent, Sanders. Big enough even for you if you think through the implications of your own positions.

And keep thinking of what that number will be for three locus traits, four locus traits, n locus traits - under selection vs the absence of selection. Just drift and nonadaptive linkage? That would require truly heroic special pleading.

The lower the number, the less selection is "required" for it to appear. As simple as that. I was generous to say three becuase usually only one gene has a much greater effect.

Now, I will never make a cartoon of my epistemology and wax about being selectionist-adaptationist. Never, dude.

It's simply stupid to belive you have found a concept so simple to explain just so many things. It's ideological. Specially with a phenomenon like the evolutionary history of life on earth.

Plus we know some fools will not let selection explain only evolution, but development, conscience, selection of universes, selection of memes....crapcrapcrapcrap. Selection can make "ultimate sense" of absolutely whatever, it seems. No sir, I'm not about to join your conga dance.

All this "drift is improbable" lithany is pretty old. .If a population is reduced drastically by a bottleneck event, the new population will be a simple expansion of that reduced genetic sample. Same thing with foundation effect. And disasters, and colonizations, are pretty common along natural history. Trust me: drift is a powerful force.

Does it ever occur to you guys that not only does the environment select variations but that it also occurs that a variation can select its environment? For innstance, a furrier bear may be able to move into colder regions; does it mean he outcompeted the non-furry? No, non-furry is right there, in the warmer climate.

I know you guys are willing to call anything natural selection, but that in fact is not natural selection. More interestingly, too, habiata preference can greatky enhance assortative mating (something your equations just never take much into account).

You may perhaps realize that adaptation is indeed something very different from selection. In fact, the most basic level at which we confirm adaptation is organismal: not populational.

The cichlid paper is pretty close to what I wanted but yet I'm a bit disappointed; They are not talking about a single "trait" but several traits, some metrical, some "geometric". So when they say "we retrieved 46 QTL" it sounds very impressive but actually these are not genes contributing to a single trait, but they are talking about "the oral jaw apparatus" in genral...not precisely a metric trait, huh.

Now you're just moving goalposts. It's unlikely that you would accept that changing the length of, say, a single bone, constitutes a new adaptation! To make a new adaptation, you have to adjust several "widgets" (traits) in the organism. Several traits = one oral jaw apparatus.

Plus for each trait, the average of the influence of a single QTL is about 35%. So we can say that in average about 3 genes explain all the morphological variation for each trait.

No, it says that at least SIX QTL have to be detected before a null model of neutral divergence can be rejected. Several metric traits comprise the adaptation. Even if each metric trait is shaped by only 3 genes, in total a complex adaptation shaped by several genes. Voilà!

Does it ever occur to you guys that not only does the environment select variations but that it also occurs that a variation can select its environment? ...I know you guys are willing to call anything natural selection, but that in fact is not natural selection.

So how do organisms gain a habitat preference for the habitat in which they just happen to have the greatest fitness? (The ultimate explanation for the trait, not how a single individual gets it)

The length of a bone would be a fine example! Give me one of those, please. A simple trait.

Windy sais:

"No, it says that at least SIX QTL have to be detected before a null model of neutral divergence can be rejected. Several metric traits comprise the adaptation. Even if each metric trait is shaped by only 3 genes, in total a complex adaptation shaped by several genes. Voilà!"

Terribe. Now you have confirmed my worst suspicions: that the selection test was made not to each trait, but to the "functional complex" as a whole. I have noticed in many studies that adpataionists authors frequently "bend the rules" to be able to include more numbers and do tests like that. I guess they just assumed that "positive" effect on a isolated trait is somehow eqivalent ot "positive" effect on the whole funtional complex.

I'm not moving goalposts, Windy. This is simply bad stuff. It fails to convinve me, honestly. If I cannot accept their most basic assumptions, I cannot accept their "evidence" for directional selection.

"So how do organisms gain a habitat preference for the habitat in which they just happen to have the greatest fitness? (The ultimate explanation for the trait, not how a single individual gets it)

a) selectionb) driftc) pleiotropyd) magic"

ARe you being serious? Those are your only options? How about epigenetic learning of behavious? How about the capacity that organisms have of coming up with new moprhologies, either by mutation or by environmental induction of a newmorph? These things happen in real time; as well as habitat preference. Do you know anything about actual biology?

"The fact that phenotypic evolution can be studied on a character by character basis suggests that the body is composed of locally integrated units. These units can be considered as modular parts of the body which integrate functionally related characters into units of evolutionary transformation. These units may either emerge spontaneously by self-organization, or may be the product of natural selection. A selection scenario that could explain the origin of modular units needs to explain the differential suppression of pleiotropic effects between different modules and the augmentation of pleiotropic effects among the elements within the module. Four scenarios are discussed: selection for adaptation rate, constructional selection, stabilizing selection and a combination of directional and stabilizing selection. It is concluded that a combination of directional and stabilizing selection is a prevalent mode of selection and a likely explanation for the evolution of modularity."

Terribe. Now you have confirmed my worst suspicions: that the selection test was made not to each trait, but to the "functional complex" as a whole.

Jesus H. tap dancing Christ. So now you don't want an example of a complex adaptation shaped by several genes? This is just useless.

"a) selectionb) driftc) pleiotropyd) magic"ARe you being serious? Those are your only options?

No, you edited out e) ? (other)

How about epigenetic learning of behavious? How about the capacity that organisms have of coming up with new moprhologies, either by mutation or by environmental induction of a newmorph?

So how do these "behavious" lead to a habitat preference FOR THE HABITAT IN WHICH THE ANIMAL'S FITNESS IS GREATEST? Do you not realize that learning, habitat preference and phenotypic plasticity evolve as well as the phenotype?

Let's take an easier example than bears: the peppered moth. If there exists a preference to a resting site that mirrors the moth's own colouration, as has been suggested by some authors, how did the moths gain this preference? Was that "learning" too?

The extended phenotype concept does not truly face the consequnces of that insight (originally discussed by Von Uexkull and a bit by Mayr) but rather finds the way to ignore it an bring it all back to gene selectionby taking gentic reductionsim to a new level of stupidity, greater than what he had already achieved with his "selfish gene" monstrosity.

Tupai, I have no idea what is your point about modularity, but let me take this WILD guess..SELECTION explains THAT too!! Yipppeeeee!!!

Let's stick with dicussing field examples or you guys are simply going to bore me to death.

I have no intention of explaining the alternatives.It is useless with people who obviously and shamelessly are set but on one thing: to bring it all down to selection. I know perfectly well what kind of fools you are.

Windy, simply two things: 1) I am NOT asking for a complex adptation, darling. I said the lenght of a bone was fine, what were you doing, sucking on some toffe when I said that?.

2) The pepper moth is a case where the environment selects variations; all I said is that it also occurs, that variations select their environment; organic change, genetic or epigenetic, can lead to an inmediate preference of a new aspect of its habitat and some degree of isolation, without a process of competition or elimination of other forms. Is that so hard to parse? Pus I have made no claims as to whether fitness increases or not in these new kinds; and you shouldn't either; but becaase you are a adaptationists, you just assume it MUST always increase. You are wrong, both theoretically and empirically.

The pepper moth is a case where the environment selects variations; all I said is that it also occurs, that variations select their environment; organic change, genetic or epigenetic, can lead to an inmediate preference of a new aspect of its habitat and some degree of isolation, without a process of competition or elimination of other forms. Is that so hard to parse?

The peppered moth colour variants are selected by the environment but the peppered moth also selects its environment through habitat preference. Is that so hard to parse?

These things happen in real time; as well as habitat preference. Do you know anything about actual biology?

Yeah, screw you too. I have a PhD in biology and I work in research.

I almost think it serves Larry right to have his adaptationist-baiting threads invaded by this goldschmidtian troll :)

Do you think there are any biologists who believe that every visible mutation must be subject to selection? For example, do you think that Richard Dawkins could ever say something like this?

The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's 'neutral mutations' are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

Read carefully. This—possibly hypothetical—scientist is saying that if there's a phenotype then it can't be neutral.

According to you, there are no scientists who hold this position. Right?

Sanders, if the giant panda had just been discovered I bet that "mutationists" would have immediately assumed that its "thumb" is a Batesonian meristic mutation. As we all know, it isn't. Instead, it is testimony to the shaping power of selection acting on preexisting developmental programs. In fact, similar selective forces acting on the carnivore paw independently produced a similar mechanism of developmental change in the unrelated red panda.

(Do the thumbs of the two pandas also show that developmental programs bias the pathways selection-directed evolution can take? Sure.)

Let me correct my earlier post - the thumb of the red panda originally aided in arborealism, a preadaptation to object manipulation.

http://www.pnas.org/cgi/content/full/103/2/3791

As for shaped by selection, this will be settled by developmental genetics. (I doubt that the fossil record will be so complete.)

What is with your fixation with the single step? Identifying the probable developmental trajectory of a trait change does not necessarily imply that such change must occurred in a single step, whether the trait in question is a pedomorphic hair pattern or a false thumb. The evolutionary expression of such a trajectory in any given case may well be - and in scores of cases, certainly was - in stages.

Read carefully. This—possibly hypothetical—scientist is saying that if there's a phenotype then it can't be neutral.

According to you, there are no scientists who hold this position. Right?

Larry I think you have to read your copy of The Extended Phenotype again. In fact if you google the passage you cite you can look it up in google books.

Dawkins says:"Adaptationist thinking, if not blind conviction, has been a valuable stimulator of testable hypothesis in physiology" and "I have tried to show that adaptationism can have virtues as well as faults" and "But this chapter's main purpose is...to list the main reasons why the student of adaptation should proceed with caution"

The two sentences just prior to what you cite might help to clarify:"If there are neutral mutations in the biochemists' sense, what this means is that any change in polypeptide structure which they induce has no effect on the enzymatic activity of the protein. This means that the neutral mutation will not change the course of embryonic development, will have no phenotypic effect at all as a whole organism biologist would understand phenotypic effect."

That is what he is referring to when he states: "If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists. In other words he cannot be dealing with neutrality because there is a phenotypic effect. In the biochemists sense neutrality means there is no phenotypic effect.

The very next sentences after your quotation are: "He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral.

Now I have no right to be getting in on an argument between biologists of any stripe so I apologize if I have grossly misread this but it seems that you have misunderstood Dawkins' point. Maybe you should take your own advice and read carefully (or maybe I should just butt out).

In my last post this paragraph should have included an end quotation after the words biochemical geneticists:

That is what he is referring to when he states: "If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists."

The following sentences were written by me not Dawkins: In other words he cannot be dealing with neutrality because there is a phenotypic effect. In the biochemists sense neutrality means there is no phenotypic effect.

To me the problem with adaptationism is very simple: it is false that adaptation = result of natural selection. This unfortunate misunderstanding continuously presents the adaptationist with the tempation of considering a selective hypotheses as a "sufficient" explanation for the origin of any adaptation. His mind classifies everything else as secondary, footnote knowledge. Dawkins is such an adaptationist.

in case you didn't read the PNAS article referred to above, from the text:Using these observations and assigning a Darwinian fitness coefficient of 1.0 to the women with the high-saturation genotype, the relative Darwinian fitness of women with the low-saturation genotype was only 0.44. For comparison, in the classic case of an environment with endemic falciparum malaria, a Darwinian fitness coefficient of 0.66 applies to homozygotes for normal hemoglobin A (51). High-altitude hypoxia may be an even stronger agent of natural selection than falciparum malaria. These findings suggest that the frequency of the high saturation allele maybe increasing rapidly in the Tibetan population.

I don't know who you are talking to because that phrase "Oh no, the last two are not "evolution in action." is not mine. I consider the PNAS article to make some interesting comparsions to andeans, and it's good they hunted down a hig saturation allele that is being selected.

But is selection all there is to high altitude adaptation? If we think that mutations become readily available for selection to favor, it is kind of weird that a younger high-altitude population, the andeans, offer no evidence for ongoing selection of any allele. This is what makes me suspect that mutations are discrete events (they are not always there) and that differences in the previous genetic compositions of both populations ("preadaptation", if you wish) are very relevant to this story.

Tupaia, your case with the panda thumbs simply demonstrates nothing. That's what I expect from an adaptationists: a theory of everything is a theory of nothing.

Sanders: "If we think that mutations become readily available for selection to favor"

That's a cartoon of selectionism.

Sanders: "mutations are discrete events (they are not always there) and that differences in the previous genetic compositions of both populations ... are very relevant to this story."

That's hardly news. Tell us something we don't know.

Panda's thumb: The moral of the story is not to make a default assumption of meristic mutation.

Razib, this is where Sanders is coming from (to save you the discovery process):

"Nor do complex adaptations constitute in themselves evidence for selection shaping an adaptation."

"(A) few mutations with large effect are behind the origin of new adaptations. In fact, there is no example that I know of where an adaptation has been shown to be have been shaped by an accumulation of several genes by natural selection."

In his view, selection does not produce or shape adaptations; it only increases or decreases the frequency of genotypes. Adaptations based on multiple loci are not evidence of selection; but rather drift and (nonadaptive) linkage.

Sanders rejects the positions of Gould and West-Eberhard as too orthodox. His views appear to be closest to Richard Goldschmidt, with nods to Francisco Varela (autopoiesis) and Stuart Kauffman (self-organization).

"Adaptations based on multiple loci are not evidence of selection; but rather drift and (nonadaptive) linkage"

Not true. They could perfectly constitute evidence for selection, specially if we have evidence of the corresponding selective condition, which is titally doable.

I ask, please, for the third time: Give me an example of a SIMPLE polygenic adaptation that has been shaped by selection.I think my objection of the cichlid paper was clear enough. I am noit unfarily rejecting the case: Ia m questioning the assumption the oral jaw apparatus can be considered a metric trait o which the ACTUAL metric ttraits that compose it make and always "postive" contribution: only if they do this can they apply the test of selection they consider as "evidence".I guess Sven and Windy are simply not smart enough to understand this objection. It already flew right past their heads once.

P.D. any frivolous attempt to label me will remain futile and pointless.

"The apparent duplication of a structure does not necessarily mean that it occurred with a single regulatory mutation"

There could be a previous buildup of mutations up to a certain threshold, but when a homeotic transformation occurs, it is a qualitative, non-gradual change. Traits usually found in one part of the body now develop in another.

kaufman is also these guys that plunge into models and do not deal w¡enough with natural history. If Kaufman knew a bit more natural history, he may nt have been convinced by Manyard Smith. One biomathematician convinced another? Not so surprising. Models resist a lot. None of those guys has truly trustsnatural history. In this sense I am much more likely to sympathize with the very darwinian Mayr than with those guys.

HUH. I get you. Natural homeotic transformations in evolution are "apparent". They have been shaped by selection. They just happen to look exactly like the homeotic transfomations we can achieve in the lab. What a coincidence.

I ask, please, for the third time: Give me an example of a SIMPLE polygenic adaptation that has been shaped by selection.I think my objection of the cichlid paper was clear enough. I am noit unfarily rejecting the case: Ia m questioning the assumption the oral jaw apparatus can be considered a metric trait o which the ACTUAL metric ttraits that compose it make and always "postive" contribution: only if they do this can they apply the test of selection they consider as "evidence".I guess Sven and Windy are simply not smart enough to understand this objection. It already flew right past their heads once.

No, we noticed you pulled "metric trait" right out of your ass. What you originally said was:

I'm more interested in the case where directional selection is supposed to accumulate genes with small phenotypic effects, to thus produce an important adaptive difference between sibling species.

No mention of a single metric trait. But if you want a metric trait responding to selection, what's wrong with the entire fucking history of agriculture?

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.